mrca

getMRCA

<code>mrca</code> returns for each pair of tips (and nodes) its most
 recent common ancestor (MRCA).
<code>getMRCA</code> returns the MRCA of two or more tips.

manip

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Emmanuel Paradis

Analyses of Phylogenetics and Evolution

Simon Blomberg

Ben Bolker

Joseph Brown

Santiago Claramunt

Julien Claude

Hoa Sien Cuong

Richard Desper

Gilles Didier

Benoit Durand

Julien Dutheil

RJ Ewing

Olivier Gascuel

Thomas Guillerme

Christoph Heibl

Anthony Ives

Bradley Jones

Franz Krah

Daniel Lawson

Vincent Lefort

Pierre Legendre

Jim Lemon

Guillaume Louvel

Federico Marotta

Eric Marcon

Rosemary McCloskey

Johan Nylander

Rainer Opgen-Rhein

Andrei-Alin Popescu

Manuela Royer-Carenzi

Klaus Schliep

Korbinian Strimmer

Damien de Vienne

mrca function

<dl> <dt>phy</dt>
<dd>an object of class <code>"phylo"</code>.</dd> <dt>full</dt>
<dd>a logical indicating whether to return the MRCAs among
 all tips and nodes (if <code>TRUE</code>); the default is to return only
 the MRCAs among tips.</dd> <dt>tip</dt>
<dd>a vector of mode numeric or character specifying the tips;
 can also be node numbers.</dd></dl>

Arguments

Emmanuel Paradis, Klaus Schliep, Joseph W. Brown

Author

Find Most Recent Common Ancestors Between Pairs — mrca

<dl>

 <dt>phy</dt>
<dd>an object of class <code>"phylo"</code>.</dd>

 <dt>full</dt>
<dd>a logical indicating whether to return the MRCAs among
 all tips and nodes (if <code>TRUE</code>); the default is to return only
 the MRCAs among tips.</dd>

 <dt>tip</dt>
<dd>a vector of mode numeric or character specifying the tips;
 can also be node numbers.</dd>

</dl>

Find Most Recent Common Ancestors Between Pairs

mrca: Find Most Recent Common Ancestors Between Pairs

Description

Usage

Value

Arguments

Author

Details